猫科动物DNA条形码及线粒体假基因对物种鉴定的影响

DNA Barcoding in Felidae,and the Effects of Nuclear Mitochondrial Pseudogenes on Species Identification

在多种动物类群中,基于线粒体细胞色素c氧化酶亚基Ⅰ(COⅠ)基因的DNA条形码是一种高效的物种鉴别手段,然而猫科Felidae动物中广泛存在的线粒体假基因可能影响DNA条形码的有效性。本研究共涉及猫科动物12属25种119个样本。采用3对条形码通用引物对6属11种29个猫科动物样本进行了扩增及测序。结果3个样本扩增失败,8个样本得到假基因,18个样本获得了条形码序列。结合另外93条猫科动物条形码序列(源自BOLD Systems),采用Kimura 2-parameter模型计算遗传距离,构建Neighbor-Joining(NJ)树。结果显示,遗传距离种内为0%~8.1%,平均0.8%;种间为1.4%~13.1%,平均8.7%;属间为8.2%~21.8%,平均15.1%。NJ树显示,除3个种外,其余物种均以极高的置信度(99%)形成单系分支。而假基因序列有些可以单独形成分支,有些夹杂在COⅠ序列形成的分支中,对物种鉴定产生干扰。

In a variety of animal species,DNA barcoding based on mitochondrial cytochrome c oxidase subunit Ⅰ（ COⅠ）gene is an efficient tool for species identification. However,the presence of large mitochondrial pseudogenes in felids may affect the effectiveness of DNA barcoding. In this study,119 felid samples from 25 species of 12 genera were analyzed.3 pairs of universal primers were used to amplify and sequence the COⅠ genes of 29 felid samples that belonged to 11 species from 6 genera. The results showed that the amplification was failed in 3 samples,nuclear mitochondrial psedogenes（ numts） were obtained in 8 samples,and barcode sequences were derived in 18 samples. Combined with the other 93 felid barcode sequences（ derived from BOLD Systems）,Kimura 2-parameter model was used to calculate the genetic distance and to construct Neighbor-Joining（ NJ） tree. The genetic distance within species were 0%-8. 1%,with an average of0. 8%; the interspecific genetic distance were 1. 4%-13. 1%,with an average of 8. 7%; and the genetic distance within family were 8. 2%-21. 8%,with an average of about 15. 1%. The NJ tree showed that most of the species formed a monophyletic clade with high confidence（ 99%）,except 3 species; some of the numts sequences could form a clade on NJ tree,and the others were inserted in the branches of the COⅠ sequences,which may compromise the species identification.